My Goodness My Guinea-ness?

Update: After this post a researcher who is planning on publishing work on the genetic structure of Great Britain and Ireland and who has a very large N forwarded me a PCA which he gave me permission to repost. I’ve uploaded it here.

As you might infer from the post below I’ve started to get interested in African population structure. It’s not just me. Readers regularly query me about the relationship of various groups, such as the Nilotic peoples who reside amongst the Bantu in northeast Africa. Additionally, there is a consistent problem with 23andMe generating weird results for people of African ancestry, usually those with East African ancestry.

But to figure out the nature of African variation in more detail we also need to give some thought to outgroups. My initial assumption was that using Tuscans would be sufficient, but several people pointed out that many Mediterranean groups have trace African admixture. Probably not enough to matter, but why take the risk? So how about looking to Northern Europe? The Utah Whites and Orcadians jump out as plausible alternatives, but there was a third which I thought I’d try out: the Irish.

Last fall my friend Paul bought a bunch …

Fighting stupid with stupid

When I discuss archaeogenetics with people they often automatically bring their preconceptions to the table, and reframe my own position in a way to make it more intelligible to them. For example, the ground-breaking paper Reconstructing Indian Population History shows that modern South Asians can be viewed very confidently as a compound between two parent populations which synthesized at some point in the past. These are termed “Ancestral North Indians” and “Ancestral South Indians.”

Several Indians I’ve discussed this issue with on the internet have expressed anger at the ANI-ASI model, suggesting that I support the “discredited ‘Aryan invasion theory’”. There’s an interesting point: I invariably avoid referring to the ANI as Indo-Aryans because I don’t think they were Indo-Aryans. My own position, held with only moderate confidence, is that the ANI pre-date the intrusion of Indo-European populations to the Indian subcontinent. Granted, I do think that Indo-Europeans are exogenous. That is, their point of origin was probably not in India, but rather in Central Asia. There are various reasons I hold to this position, but the biggest issue I have with Indians is that they behave as if the rest of the world does not exist. All their arguments for the indigenous status of Indo-Europeans to India could apply to the Indo-European Greeks (e.g., the Greeks have no memory of a land before Hellas). But that is neither here nor there.

European Misappropriation of Sanskrit led to the Aryan Race Theory:

In 2007, I played a role in a historic milestone when I was invited to address the first Hindu-Jewish Summit. I spoke on the Aryan myth and the suffering that it had inflicted on both religious communities. Contrary to earlier apprehensions of some Hindus that this was a “risky” topic to bring up, the head of the Jewish delegation, Rabbi Rosen, member of the Chief Rabbinate of Israel’s Commission for Inter-religious Dialogue, was very impressed. The Jewish delegation decided to appoint a team of scholars to study the issue and the references I had supplied. As a result, at the following year’s Summit, a joint declaration was signed, which included the following language from my draft:

“Since there is no conclusive evidence to support the theory of an Aryan invasion/migration into India, and on the contrary, there is compelling evidence to refute it; and since the theory seriously damages the integrity of the Hindu tradition and its connection to India; we call for a serious reconsideration of this theory, and a revision of all educational material on this issue that includes the most recent and reliable scholarship.”

Much of Hindu tradition is a bunch of primitive superstition (and personally I think Vedanta is sophisticated superstition, like almost all of religiously inflected philosophy). Who cares? And before some Hindus bellyache, how about you enjoy this cute reedit:

The forgotten East, part 2

A month ago I posted India East and Inward. On a related vein, over at Discover a commenter observes:

It is interesting that four individuals have some African ancestry, no doubt due to the slave trade. The Carribean individual acquired it from the European slave trade and the Sindhi and Balochi individuals from the Islamic slave trade.

But what about the E. Asian component? History and geography can explain its presence in Razib’s parents and in Bengali individuals. According to Reich et al. South Asians can be modeled as a linear combination of ANI and ASI or in this model a linear combination of S. Asian and European. The ASI is quite distinct from E. Asian. Why is there some E. Asian in most individuals? Is this real or is it an artifact of the ADMIXTURE analysis?

My response:

first, reich et al. know that there are other minor elements. that’s why they discard outliers which have these minor elements to a great enough extent. second, i assume that it is noise in most of the cases. but some of the south indian samples (tribes) look way too admixed to be noise. the slave trade probably came from southeast asia too. in sri lanka malays have preserved their cultural identity, just as they have to some extent in south africa (less so), but probably this percolated in parts of south india. we aren’t surprised when we see west asian among kerala christians. we should be less surprised if we see some southeast asian in the tamil country.

The Bantu völkerwanderung

Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an …

The New York Times “pay wall”

So what do readers of this blog think? Pay or no pay? It’s useful, and The New York Times is pretty massive in scope, if sometimes lacking in breadth. I love their data-oriented stuff, but I ignore their columnists and a lot of their “analysis,” which is frankly substandard if I know anything about the topic (which suggests to me if I don’t know about the topic, they barely do too). There are certain areas where blogs have a comparative advantage, and I don’t see why an organization with other strengths would even make an attempt.

Personal genomics gets very personal

Dan MacArthur points me to this nice post over at Daily Kos, Our Genome Decoded: How Companies Like 23andMe Are Advancing the Field of Personal Genomics:

…However, in the past few years several private biotech companies have started offering a “personal genome service” that involves sequencing the most variable portions of our DNA. The goals are straightforward – to give individuals information about their ancestry and inherited traits. While there are definite limitations – both technically and bioethically – to the amount and type of information that can be obtained from personal genome sequencing, in my case the service answered a lingering question about something important to me, and thus was well worth it.

In this article, I’m going to tell the story about why I chose to purchase a personal genome service, briefly explain how it works, show my interesting results, and finally, provide some commentary on how these services will impact the fields of genomics and medicine.

One step at a time. I also appreciate that Michelle keeps posting on her ADMIXTURE results.

Bravo for Mormons!

Trying to Relish the Big Time, Even When It Brings a Cringe:

The house lights came up and it was intermission at “The Book of Mormon,” the new Broadway musical about a pair of innocent young Mormon missionaries sent to Uganda to spread the faith. John Dehlin, a graduate student who flew in from Utah to see the show with a group of Mormons from around the country, was still riveted to his theater seat, having flashbacks.

“It’s way, way too close to home,” he said, recalling his own missionary years in Guatemala: the shock at the poverty and violence, the pressure from the mission president to baptize more natives, the despair when his mission companion ran off with a local girl — and the Mormon mandate, above all, to repress doubt and remain relentlessly cheery.

A friend in the crowded theater aisle, Paul Jones, passed by and gave Mr. Dehlin a high-five and a hug. “It’s right on,” said Dr. Jones, a dentist from Gilbert, Ariz., “but I cringed a little bit, a couple of times.”

The arrival of a Broadway musical that ridicules their religion, produced by the creators of the scathingly satirical television show “South Park,” is proving to be …


Indian film stars vs regular Indians:

A couple of points about the article. I disagree that the obsession with fair skin is related to British colonialism to any great degree. Preference for “lightness” does not equate to preference for “whiteness”. It’s far older than British rule and has its basis in the caste system. The conquerors of India have historically come from the north (Indo-Europeans, Muslim Moghuls), and the darker tones of the Southern Indians have acquired a negative association, enshrined by caste. It is probably overlain with an element of the same colour prejudice that occurs in East Asia, which is related to social class and occupation (dark skin = tan from working out in the sun = being a commoner).

Realistically, the likes of Sharma, Gracias and Rajandran are not really dark, when one considers the diversity of phenotypes across India. They are probably in the middle of the skin tone range. The ideal look for Indian celebrities is at the pale end of the spectrum. Male actors can to some extent get away with a degree of swarthiness that females can’t. Still, in a country with significant prejudices against its Muslim minority and hatred towards its Muslim neighbour Pakistan, some of the biggest male stars of Bollywood are Muslims (Aamir Khan, Salman Khan, Shah Rukh Khan), and I wonder how much that is related to their “Aryan”-ness.

Tipu Sultan, a "black" Muslim

It is correct that the preference for light skin predates the British era. Blaming something on colonialism is such a lazy trope. From the Muslim period there’s enough textual evidence to indicate that the Iranian and Turanian ruling caste had contempt for the natives on racial as well as religious grounds. From what I have read there was even some hostility directed at the South Indian Muslim warlord Tipu Sultan because of his clear origins among Hindu converts. The painting to the left makes no effort mask his rich brown pallor.

Whether this attitude toward light skin predates Muslim period is more contested. There is a strong strain of older scholarship which suggests that ancient Hindu texts and traditions do suggest contempt toward the dark-skinned peoples of the subcontinent. Revisionists, often of Indian nationalist bent, have reinterpreted the conflict between the light and the dark in metaphorical terms. For me the recent genetic data indicating partitioning between high and low castes in any given region implies that the view that differences in color were pure metaphor is probably not correct, and there was some genuine racial element even in the antique period. I suspect that the underlying reason is the one given above, that so many military elites in South Asian history have had a northwestern origin. Assam might be an interesting contrast, because the Ahom are Sino-Tibetan, though even in this case the elites would have been lighter skinned.


The end of Ayla & The Land of Painted Caves

I read  Jean Auel’s Clan of the Cave Bear in elementary school at a friend’s house during a sleep over. It was next to the bedside, and I decided to pick it up. I’d thought it was a human evolution book from the cover. I read  2/3 of the book by dawn, took a few hours to catch up on sleep, and then finished the rest before the afternoon. I read almost no fiction outside of what was assigned in school as a child, but this was the exception (I also read a lot of Greek mythology, though I’m not sure that counts). The three sequels I finished in middle school when I noticed there were sequels! By the time book 5, Shelter of the Stones, came out in the early aughts I’d lost interest. I’ve moved on, but many have not. The last book, The Land of Painted Caves, is now out. The Los Angeles Times has written a retrospective of the series.

Since Amazon has a 1 to 5 star rating system, I thought I’d plot the results for the first five books. On the y-axis you have the number who gave …